Install log for 'hipread'

* installing *source* package ‘hipread’ ...
** this is package ‘hipread’ version ‘0.2.4’
** package ‘hipread’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/hipread/src'
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c column.cpp -o column.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c datasource.cpp -o datasource.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c gzstream.cpp -o gzstream.o
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/deprecated_macros.hpp:8,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/sp_counted_base.hpp:22,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:22,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17,
                 from boost.h:12,
                 from datasource.h:8,
                 from hipread_types.h:4,
                 from RcppExports.cpp:4:
/data/gannet/ripley/R/test-dev/BH/include/boost/detail/atomic_count.hpp:10:1: note: ‘#pragma message: This header is deprecated. Use <boost/smart_ptr/detail/atomic_count.hpp> instead.’
   10 | BOOST_HEADER_DEPRECATED("<boost/smart_ptr/detail/atomic_count.hpp>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/deprecated_macros.hpp:8,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/sp_counted_base.hpp:22,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:22,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17,
                 from boost.h:12,
                 from column.h:6,
                 from column.cpp:4:
/data/gannet/ripley/R/test-dev/BH/include/boost/detail/atomic_count.hpp:10:1: note: ‘#pragma message: This header is deprecated. Use <boost/smart_ptr/detail/atomic_count.hpp> instead.’
   10 | BOOST_HEADER_DEPRECATED("<boost/smart_ptr/detail/atomic_count.hpp>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c iconv.cpp -o iconv.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c read_chunked.cpp -o read_chunked.o
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/deprecated_macros.hpp:8,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/sp_counted_base.hpp:22,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:22,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17,
                 from boost.h:12,
                 from datasource.cpp:7:
/data/gannet/ripley/R/test-dev/BH/include/boost/detail/atomic_count.hpp:10:1: note: ‘#pragma message: This header is deprecated. Use <boost/smart_ptr/detail/atomic_count.hpp> instead.’
   10 | BOOST_HEADER_DEPRECATED("<boost/smart_ptr/detail/atomic_count.hpp>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c read_freqs.cpp -o read_freqs.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c read_full.cpp -o read_full.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c read_yield.cpp -o read_yield.o
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/deprecated_macros.hpp:8,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/sp_counted_base.hpp:22,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:22,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17,
                 from boost.h:12,
                 from column.h:6,
                 from read_chunked.cpp:2:
/data/gannet/ripley/R/test-dev/BH/include/boost/detail/atomic_count.hpp:10:1: note: ‘#pragma message: This header is deprecated. Use <boost/smart_ptr/detail/atomic_count.hpp> instead.’
   10 | BOOST_HEADER_DEPRECATED("<boost/smart_ptr/detail/atomic_count.hpp>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c rtinfo.cpp -o rtinfo.o
g++ -std=gnu++17 -I"/data/gannet/ripley/R/R-devel/include" -DNDEBUG  -I'/data/gannet/ripley/R/test-dev/Rcpp/include' -I'/data/gannet/ripley/R/test-dev/BH/include' -I/usr/local/include    -fpic  -g -O2 -Wall -pedantic -mtune=native -Wno-ignored-attributes -Wno-parentheses -Wp,-D_FORTIFY_SOURCE=3 -fexceptions -fstack-protector-strong -fstack-clash-protection -fcf-protection   -c varinfo.cpp -o varinfo.o
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/deprecated_macros.hpp:8,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/sp_counted_base.hpp:22,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:22,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17,
                 from boost.h:12,
                 from column.h:6,
                 from read_freqs.cpp:2:
/data/gannet/ripley/R/test-dev/BH/include/boost/detail/atomic_count.hpp:10:1: note: ‘#pragma message: This header is deprecated. Use <boost/smart_ptr/detail/atomic_count.hpp> instead.’
   10 | BOOST_HEADER_DEPRECATED("<boost/smart_ptr/detail/atomic_count.hpp>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/deprecated_macros.hpp:8,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/sp_counted_base.hpp:22,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:22,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17,
                 from boost.h:12,
                 from column.h:6,
                 from read_yield.cpp:2:
/data/gannet/ripley/R/test-dev/BH/include/boost/detail/atomic_count.hpp:10:1: note: ‘#pragma message: This header is deprecated. Use <boost/smart_ptr/detail/atomic_count.hpp> instead.’
   10 | BOOST_HEADER_DEPRECATED("<boost/smart_ptr/detail/atomic_count.hpp>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/deprecated_macros.hpp:8,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/sp_counted_base.hpp:22,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/detail/shared_count.hpp:22,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/smart_ptr/shared_ptr.hpp:17,
                 from /data/gannet/ripley/R/test-dev/BH/include/boost/shared_ptr.hpp:17,
                 from boost.h:12,
                 from column.h:6,
                 from read_full.cpp:2:
/data/gannet/ripley/R/test-dev/BH/include/boost/detail/atomic_count.hpp:10:1: note: ‘#pragma message: This header is deprecated. Use <boost/smart_ptr/detail/atomic_count.hpp> instead.’
   10 | BOOST_HEADER_DEPRECATED("<boost/smart_ptr/detail/atomic_count.hpp>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -shared -L/usr/local/lib64 -o hipread.so RcppExports.o column.o datasource.o gzstream.o iconv.o read_chunked.o read_freqs.o read_full.o read_yield.o rtinfo.o varinfo.o -lz
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/hipread/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-devel/hipread/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-devel/hipread/src'
installing to /data/gannet/ripley/R/packages/tests-devel/hipread.Rcheck/00LOCK-hipread/00new/hipread/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (hipread)